Petr Danecek

Yes, and the examples `0|1` and `0/1|2` given in the specification are the only mention of this. The "phase follows the allele" notation seems more intuitive and VCF is the...

This is partly a problem with your VCF, partly with HTSlib: 1) the header says the WP field is an integer with Number=A values. If such, the values in the...

I don't know what is the intention, but probably it would be best to redefine the tag in the header as `Type=String`. That way it will stay preserved.

Why do you need to rename your files? The suffix name does matter for the operation of the program.

Yes, it should use the magic number, this fails: ```` bgzip -d test.bgz [bgzip] test.bgz: unknown suffix -- ignored ```` As a quick workaround, use ```` gunzip -c test.bgz ````

You need to provide either the `-p` or `-s,-b,-e` options to tabix. For example `tabix -s1 -b2 -e3 file.txt.gz`

Try `sort -k1,1d -k2,2n -k3,3n`

Currently there is no other, more direct, API. The only other option would be to manipulate the hrec records directly.

@jblachly The max_unpack feature is intended for faster reading of VCFs with many samples in the special case when the program does not need to access the FORMAT fields, see...

That's an interesting case. First a general comment, the minimum PL does not have to be 0. Any normalization would be done in probability space (i.e. not in phred/log space)....